FitHiC {FitHiC} | R Documentation

## Fit-Hi-C

### Description

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

### Usage

    FitHiC(fragsfile, intersfile, outdir, biasfile = "none", noOfPasses = 1,
      noOfBins = 100, mappabilityThreshold = 1, libname = "",
      distUpThres = -1, distLowThres = -1, visual = FALSE,
      useHiCPro = FALSE)

### Arguments

`fragsfile` | The path specifies where FRAGSFILE is located in the file system. FRAGSFILE stores the information about midpoints (or start indices) of the fragments. It should consist of 5 columns: first column stands for chromosome name; third column stands for the midPoint; fourth column stands for the hitCount; second column and fifth column can be arbitrary.
`intersfile` | The path specifies where INTERSFILE is located in the file sytem. INTERSFILE stores the information about interactions between fragment pairs. It should consist of 5 columns: first column and third column stand for the chromosome names of the fragment pair; second column and fourth column stand for midPoints of the fragment pair; fifth column stands for hitCount.
`outdir` | The path specifies where the output files will be stored in the file system. If the path does not exist, it will be automatically created.
`biasfile` | The path specifies where BIASFILE is located in the file system. BIASFILE stores the information about biases calculated by ICE for each locus. It should consist of 3 columns: first column stands for chromosome name; second column stands for the midPoint; third column stands for the bias. This argument is OPTIONAL.
`noOfPasses` | Number of passes after the initial (before) fit. DEFAULT is 1 (after).
`noOfBins` | Number of equal-occupancy (count) bins. Default is 100.
`mappabilityThreshold` | Minimum number of hits per locus that has to exist to call it mappable. DEFAULT is 1.
`libname` | Name of the library that is analyzed to be used for plots. DEFAULT is empty.
`distUpThres` | Upper bound on the intra-chromosomal distance range (unit: base pairs). DEFAULT is no limit.
`distLowThres` | Lower bound on the intra-chromosomal distance range (unit: base pairs). DEFAULT is no limit.
`visual` | Use this flag for generating plots. DEFAULT is False.
`useHiCPro` | Whether to use HiC-Pro preprocessed data. DEFAULT is False.

### Value

None

### Author(s)

Ruyu Tan, rut003@ucsd.edu

### Examples

    fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Duan_yeast_EcoRI")
    FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI",
        distUpThres=250000, distLowThres=10000)

    fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_HindIII.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata", "contactCounts/Duan_yeast_HindIII.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Duan_yeast_HindIII")
    FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_HindIII",
        distUpThres=250000, distLowThres=10000)

    fragsfile <- system.file("extdata",
        "fragmentLists/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata",
        "contactCounts/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_combineFrags10_chr1")
    FitHiC(fragsfile, intersfile, outdir,
        libname="Dixon_hESC_HindIII_hg18_combineFrags10_chr1", noOfBins=200,
        distUpThres=5000000, distLowThres=50000)

    fragsfile <- system.file("extdata",
        "fragmentLists/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata",
        "contactCounts/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Dixon_mESC_HindIII_mm9_combineFrags10_chr1")
    FitHiC(fragsfile, intersfile, outdir,
        libname="Dixon_mESC_HindIII_mm9_combineFrags10_chr1", noOfBins=200,
        distUpThres=5000000, distLowThres=50000)

    fragsfile <- system.file("extdata",
        "fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata",
        "contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1")
    FitHiC(fragsfile, intersfile, outdir,
        libname="Dixon_hESC_HindIII_hg18_w40000_chr1", noOfBins=50,
        distUpThres=5000000, distLowThres=50000)

    fragsfile <- system.file("extdata",
        "fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata",
        "contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
        package = "FitHiC")
    outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1.afterICE")
    biasfile <- system.file("extdata",
        "biasPerLocus/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
        package = "FitHiC")
    FitHiC(fragsfile, intersfile, outdir, biasfile,
        libname="Dixon_hESC_HindIII_hg18_w40000_chr1", noOfBins=50,
        distUpThres=5000000, distLowThres=50000)

    fragsfile <- system.file("extdata", "fragmentLists/data_5000000_abs.bed.gz",
        package = "FitHiC")
    intersfile <- system.file("extdata", "contactCounts/data_5000000.matrix.gz",
        package = "FitHiC")
    biasfile <- system.file("extdata",
        "biasPerLocus/data_5000000_iced.matrix.biases.gz", package = "FitHiC")
    outdir <- file.path(getwd(), "data_5000000")
    FitHiC(fragsfile, intersfile, outdir, biasfile, libname="data_5000000",
        distUpThres=500000000, distLowThres=5000000, useHiCPro=TRUE)

[Package FitHiC version 1.6.0 Index]